Protein kinases play an important role in regulating most cellular functions including proliferation, cell cycle, cell metabolism, survival/apoptosis, DNA damage repair, cell motility, and response to the microenvironment. Not surprisingly kinases have been identified as oncogenes. For example, kinases such as c-Src, c-Abl, mitogen activated protein (MAP) kinase, phosphotidylinositol-3-kinase (PI3-K, PI3K, PI-3 kinase), AKT (also known as PKB), and the epidermal growth factor (EGF) receptor are commonly activated in cancer cells and are known to contribute to tumorigenesis. Many of these mutations occur in the same signaling pathway. For example, HER-kinase family members (HER1 [EGFR], HER3, and HER4) transmit signals through MAP kinase and PI-3 kinase to promote cell proliferation.
PI-3 kinases are a large family of lipid kinases comprising roughly 16 members divided into 3 classes based on sequence homology and the particular product formed by enzyme catalysis. The class I PI-3 kinases are composed of 2 subunits: a 110 kd catalytic subunit and an 85 kd regulatory subunit. Class I PI-3 kinases are involved in important signal transduction events downstream of cytokines, integrins, growth factors and immunoreceptors, and control of this pathway may lead to important therapeutic effects. Inhibition of class I PI-3 kinase induces apoptosis, blocks tumor induced angiogenesis in vivo, and increases radiosensitivity in certain tumors.
Molecular and genetic studies have demonstrated a strong correlation between the PI-3 kinase pathway (also known as PI3K-AKT pathway) and a variety of diseases in humans such as inflammation, autoimmune conditions, and cancers (P. Workman et al., Nat. Biotechnol. 2006, 24, 794-796). The PI-3 kinase pathway controls a number of cellular functions including cell growth, metabolism, differentiation, and apoptosis. Many types of cancer are thought to arise in response to abnormalities in signal transduction pathways of which the PI-3 kinase pathway is a major example.
The PI-3 kinase pathway comprises a number of enzymes including PI-3 kinase, PTEN (Phosphatase and Tensin homolog deleted on chromosome 10), and AKT (a serine/threonine kinase) all of which are involved in producing and maintaining intracellular levels of second messenger molecule PtdIns(3,4,5)P3 (PIP3). Homeostasis in the levels of this important second messenger is maintained by the interaction between PI-3 kinase and PTEN. When either PI-3 kinase or PTEN are mutated and/or reduced in activity PIP3 levels are perturbed which may act as a trigger in the development of cancer. Indeed, both PI-3 kinase and PTEN have been found to be mutated in multiple cancers including glioblastoma, ovarian, breast, endometrial, hepatic, melanoma, gut, lung, renal cell, thyroid and lymphoid cancer. Multiple studies have now shown that p110α, which is a Class IA isoform of the regulatory subunit of PI-3 kinase, is frequently over-expressed and mutated in many cancers including gliomas, colon, brain, breast, lung, prostate, gynecological and other tumor types (Y. Samuels et al., Science 2004, 304, 554). Thus, a rational approach to treating cancer relates to developing drugs that act on kinases including those of the PI-3 kinase pathway.
Another putative mechanism for cancer involving kinase dependency is through loss of a negative regulator. Perhaps the best example of this comes from tumors with mutations in the PTEN tumor suppressor gene. This gene, which is mutated or deleted in a number of different cancers, encodes a lipid phosphatase that regulates signaling through the PI-3 kinase pathway. Specifically, PTEN dephosphorylates PIP3, the product of PI-3 kinase (for review see L. C. Cantley et al., Proc. Natl. Acad. Sci. 1999, 96, 4240-4245). As a consequence of PTEN loss and the resultant increase in PIP3 levels, signal propagation through downstream kinases such as AKT is constitutively elevated. Preclinical studies suggest that this indirect mode of constitutive kinase activation in tumor cells (i.e., through loss of the PTEN suppressor gene), creates a kinase dependency analogous to that seen in tumors with direct, activating mutations in the kinase itself.
Genetic and biochemical evidence from several model systems has established that constitutive levels of AKT can regulate TOR (mTOR in mammalian systems) through phosphorylation of the tuberous sclerosis complex (K. Inoki et al., Nat. Cell Biol. 2002, 4, 648-657). Hence, tumors with loss-of-function mutations in PTEN exhibit constitutive activation of AKT, as well as other downstream kinases such as mTOR. Many such tumors in murine models have been shown to be sensitive to mTOR inhibitors (M. S. Neshat et al., Proc. Natl. Acad. Sci. 2001, 98, 10314-10319).
At the cytocellular level, the induction and/or progression of cancer appears to involve a sub-population of cells within a tumor known as cancer stem cells. Within a population of cancer cells there exist a small number of cells that are capable of fully re-establishing a tumor. These cells are called cancer stem cells and are thought to be responsible for the inability to cure cancer with current drugs. These cells are characterized as having enhanced drug efflux properties, lacking in cell cycle progression (quiescent), and possessing resistance to anoikis (apoptosis upon experiencing loss of anchorage). Cancer stem cells have been described in the literature in solid tumor types, for example, see the review and references incorporated therein by J. E. Visvader et al., Nat. Rev. Cancer 2008, 8, 755-768: “Cancer Stem Cells in Solid Tumors: accumulating evidence and unresolved questions”. Non-solid tumor cancer stem cells have also been reviewed recently, for example, see the review and references incorporated therein by J. E. Dick et al., Blood 2008, 112, 4793-4807: “Stem cell concepts renew cancer research”. To date the only documented clinical example of an approved cancer therapeutic drug that decreases cancer stem cells is Lapatinib which was shown to decrease the number of breast cancer stem cells in biopsies of women with breast tumors possessing high levels of HER2 protein (decreased from 11% down to 5% of cells) [C. Schmidt et al., J. Natl. Cancer I. 2008, 100, 694-695: “Lapatinib Study Supports Cancer Stem Cell Hypothesis, Encourages Industry Research”].
While therapeutic agents that act as modulators of signaling pathways are of clear therapeutic interest as agonists or antagonists of particular enzymes within a signaling pathway, e.g. inhibitors of PI-3 kinase, recent evidence indicates that independent mechanisms exist for providing therapeutic efficacy including, for example, oxidative stress. The generation of oxidative stress in cancer cells is a recent but well described cancer treatment approach. Examples of agents that induce such stress include clinically evaluated compounds such as buthionine sulfoximine/melphalan, imexon, arsenic trioxide, and motexafin gadolinium, and the like [see for example the review and references incorporated therein by R. H. Engel et al., Front. Biosci 2006, 11, 300-312: “Oxidative Stress and Apoptosis: a new treatment paradigm in cancer”]. Cromenones such as LY294002 and the related analog LY3035111 have been reported to induce apoptosis in tumor cells due to intracellular hydrogen peroxide production independent of their PI3 kinase inhibition activity [T. W. Poh et al., Cancer Res. 2005, 65, 6264-6274: “LY294002 and LY303511 Sensitize Tumor Cells to Drug-Induced Apoptosis via Intracellular Hydrogen Peroxide Production Independent of the Phosphoinositide 3-Kinase-Akt Pathway”]. This ability to induce oxidative stress in cancer cells is a positive attribute for an anticancer agent. Oxidative stress induction has also been demonstrated to enhance sensitivity of prostate cancer cells to nonapoptotic concentrations of the chemotherapeutic agent vincristine.
LY294002 (2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one) is a potent, non-selective inhibitor of PI-3 kinases with an IC50 of 1.4 μM (C. J. Vlahos et al., J. Biol. Chem. 1994, 269, 5241-5248). While LY294002 is an effective inhibitor of PI-3 kinase it has several undesirable attributes for clinical use including lack of aqueous solubility, poor pharmacokinetics, unacceptable toxicity, lack of tissue specificity, rapid metabolism in animals, and a synthetic route that involves the use of carbon disulfide, a highly toxic compound. As such, LY294002 has never been developed for clinical use.
A growing list of diseases including cancer can arise by epigenetically-induced changes in gene expression and cellular phenotype by mechanisms other than changes in DNA nucleotide sequence. Epigenetic effects can be controlled by three types of proteins: the writers (i.e., DNA methyltransferase which adds methyl groups to DNA), the erasers (i.e., histone deacetylase, HDAC, which removes acetyl groups from histones), and the readers (i.e., BET bromodomain proteins such as BRD2, BRD3, BRD4 and BRDT). Bromodomain proteins serve as “readers” for the chromatin to recruit regulatory enzymes such as the writers and erasers leading to regulation of gene expression. Inhibitors of bromodomain proteins are potentially useful in the treatment of diseases including obesity, inflammation, and cancer (A. C. Belkina et al., Nat. Rev. Cancer 2012, 12, 465-477).
BET inhibitors act as acetylated lysine mimetics that disrupt the binding interaction of BET proteins with acetylated lysine residues on histones (D. S. Hewings et al., J. Med. Chem. 2012, 55, 9393-9413). This leads to suppression of transcription of some key genes involved in cancer including c-MYC, MYCN, BCL-2, and some NF-kB-dependent genes (J. E. Delmore et al., Cell 2011, 146, 904-917) (A. Puissant et al., Cancer Discov. 2013, 3, 308-323). Most B-cell malignancies are associated with the activation of the c-MYC gene which is partially controlled by the PI-3 kinase-AKT-GSK3beta signaling axis (J. E. Delmore et al., Cell 2011, 146, 904-917). MYC (encompassing c-MYC and MYCN) is an oncoprotein that has been difficult to inhibit using small molecule approaches (E. V. Prochownik et al., Genes Cancer 2010, 1, 650-659). Recently it has been shown that BET inhibition prevents the transcription of MYCN, (A. Puissant et al., Cancer Discov. 2013, 3, 308-323), and blocking PI-3K enhances MYC degradation (L. Chesler et al., Cancer Res. 2006, 66, 8139-8146). Therefore, a single molecule that inhibits both PI-3K and bromodomain proteins would provide a novel and more effective way to inhibit MYC activity. FIG. 1 shows the structures of several reported BET inhibitors some of which contain the 3,5-dimethylisoxazole chemotype as the acetyl-lysine mimetic moiety (D. S. Hewings, J. Med. Chem. 2011, 54, 6761-6770) (D. S. Hewings et al., J. Med. Chem. 2012, 55, 9393-9413) (D. S. Hewings et al., J. Med. Chem. 2013, 56, 3217-3227).
Several recent reviews cover the inception and status of the bromodomain inhibitor field including D. Gallenkamp et al., ChemMedChem 2014, 9, 438-464 and S. Muller et al., Med. Chem. Commun. 2014, 5, 288-296.
The need for better treatments for cancer and other diseases has lead to combination therapies using multiple anticancer agents, or alternatively multitargeting agents in which a single drug blocks more than one target (see D. Melisi et al., Curr. Opin. Pharm., 2013, 13, 536-542).
Recently, it has been shown that some kinase inhibitors also inhibit bromodomain proteins. For example, PI3 kinase inhibitor LY294002 was found to modestly inhibit BET bromodomains (A. Dittmann et al., ACS Chem. Biol. 2014, 9, 495-502). Replacement of the morpholine group of LY294002 with a piperizine group (LY303511) causes it to lose PI3K inhibition activity but retain BET bromodomain inhibition. The morpholine ring is critical for binding in the PI3K catalytic pocket and cannot be replaced even by the structually similar thiomorpholine (C. J. Vlahos et al., J. Biol. Chem. 1994, 269, 5241-5248). Other kinases have also been shown to have some BET inhibition activity. For example the PLK1 inhibitor BI2536 and the JAK2 inhibitor TG101209 also potently inhibit the BET protein BRD4-1 (S. W. J. Ember, ACS Chem. Biol. 2014, 9, 1160-1171). However, the ability of kinase inhibitors to inhibit bromodomain proteins is not a general property. As demonstrated by a recent study, of 628 kinase inhibitors tested only 7 inhibitors, namely BI2536, BI6727 (volasertib), the RSK inhibitor NI-F1870, the JAK inhibitor TG-101348, the FAK inhibitor PF-431396, the beta-isoform selective PI3K inhibitor GSK2636771, and the mTOR kinase inhibitor PP-242, showed some degree of BRD4-1 inhibitory activity (P. Ciceri et al., Nat. Chem. Biol. 2014, 10, 305-312).
There remains a need for potent inhibitors of bromodomain proteins, especially BRD4, as well as a need for small molecules that inhibit both bromodomain proteins and PI3K especially ones that inhibit both PI3K and BRD4.